install.packages("igraph")
library(igraph)
g1 <- read.graph("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AbstractsCovid19.graphml", format="graphml")
library(igraph)
V(g1)
library(igraph)
nodesofinterest <- c("therapeutic vaccine", "vaccine candidate")
# select the nodes having these names
nodesselection <- V(g1)[label %in% nodesofinterest]
# get their neighborhood
egoneighborhood <- ego(g1, order=1, nodes = nodesselection, mode = "all", mindist = 0)
# turn the returned list into a graph
egoselection <- induced_subgraph(g1,unlist(egoneighborhood))
V(egoselection)
install.packages("GGally")
library(GGally)
install.packages("sna")
library(sna)
library(network)
library(intergraph)
ggnet2(egoselection, mode = 'fruchtermanreingold', node.size="weightlinks", node.color = "cluster", label = "label", label.size=2.5, palette="Dark2", alpha = 0.75, edge.alpha = 0.2, size.legend = NULL, size.min = 1000) + theme(legend.position = "none")
install.packages("sigmajs")
library(sigmajs)
reducedgraph <- "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/VaccineGraphReduced.gexf"
vaccineInteractive <- sigmajs() %>%
sg_from_gexf(reducedgraph) %>%
sg_settings(drawLabels = TRUE, drawEdges = FALSE, labelThreshold = 4, labelSize = 10)
vaccineInteractive
library(sigmajs)
cluster1graph <- "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/Cluster1.gexf"
cluster1interactive <- sigmajs() %>%
sg_from_gexf(cluster1graph) %>%
sg_settings(drawLabels = TRUE, drawEdges = FALSE, labelThreshold = 4, labelSize = 10)
cluster1interactive
install.packages("networkD3")
## Installing package into '/usr/local/lib/R/site-library'
## (as 'lib' is unspecified)
library(networkD3)
edges <- read.csv(file ="https://raw.githubusercontent.com/mdurazob/covidnotebook/master/edgescluster1.csv")
nodes <- read.csv(file = "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/nodescluster1.csv")
d <- sankeyNetwork(Links = edges, Nodes = nodes, Source = "Source", Target = "Target",
NodeID = "name", Value = "Weight", # LinkGroup = "colour", (use if you want to colour edges)
fontSize = 14, fontFamily = "sans-serif", width = "100%")
d
install.packages("highcharter")
library(highcharter)
inhibitionpapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/InhibitionPapers.csv")
inhibitionchart <- inhibitionpapers %>%
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}")
library(highcharter)
install.packages("treemap")
library(treemap)
install.packages("viridis")
library(viridis)
install.packages("RColorBrewer")
library(RColorBrewer)
adepapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/ADEPapers.csv")
hchart(adepapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>%
hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
maxColor = brewer.pal(9, "Blues")[9])
library(highcharter)
animalmodelspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AnimalModelsPapers.csv")
animalmodelschart <- animalmodelspapers %>%
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}")
animalmodelschart
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)
therapeuticspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/therapeuticspapers.csv")
hchart(therapeuticspapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>%
hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
maxColor = brewer.pal(9, "Blues")[9])
library(highcharter)
economicspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/economicsPapers.csv")
economicschart <- economicspapers %>%
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}")
economicschart
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)
standarizationpapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AnimalStandardized.csv")
hchart(standarizationpapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>%
hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
maxColor = brewer.pal(9, "Blues")[9])
library(highcharter)
prophylaxispapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/prophylaxispapers.csv")
prophylaxischart <- prophylaxispapers %>%
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}")
prophylaxischart
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)
aftervaccinepapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/aftervaccinepapers.csv")
hchart(aftervaccinepapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>%
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>%
hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
maxColor = brewer.pal(9, "Blues")[9])